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Volumn 301, Issue 5641, 2003, Pages 1914-1918

Sequence-dependent pausing of single lambda exonuclease molecules

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINETRIPHOSPHATE; ELECTROPHORESIS; PROBABILITY;

EID: 0141534308     PISSN: 00368075     EISSN: None     Source Type: Journal    
DOI: 10.1126/science.1088047     Document Type: Article
Times cited : (129)

References (29)
  • 8
    • 0032582494 scopus 로고    scopus 로고
    • M. D. Wang et al., Science 282, 902 (1998).
    • (1998) Science , vol.282 , pp. 902
    • Wang, M.D.1
  • 9
    • 0035909370 scopus 로고    scopus 로고
    • D. E. Smith et al., Nature 413, 748 (2001).
    • (2001) Nature , vol.413 , pp. 748
    • Smith, D.E.1
  • 10
    • 0037057630 scopus 로고    scopus 로고
    • T. Ha et al., Nature 419, 638 (2002).
    • (2002) Nature , vol.419 , pp. 638
    • Ha, T.1
  • 11
    • 0141542823 scopus 로고    scopus 로고
    • note
    • Materials and methods are available as supporting material on Science Online.
  • 13
    • 0141431137 scopus 로고    scopus 로고
    • note
    • A force clamp supplies improved resolution over open-loop systems and makes it unnecessary to apply corrections for the elastic compliance of the DNA-motor complex (12). Force clamps based on stage motion, as opposed to those that steer the optical trap by acousto-optic deflectors (28), are well suited to studying slow-moving, processive enzymes, because they afford a greater operating range (>10 μm) together with high precision (∼2 nm) at the cost of reduced feedback loop closure time (∼0.1 s).
  • 14
    • 0141431136 scopus 로고    scopus 로고
    • note
    • The velocity was unchanged by a threefold increase in force from 1 pN (fig. S1A). This insensitivity to external load was observed for several molecules (fig. S1B) and implies that the mechanical translocation step of the reaction cycle is not rate-determining at low loads. A similar finding has been reported for RNA polymerase (8). Force-velocity analysis over a greater range was not possible because tethered complexes failed to support significant loads (>3 pN) for extended periods (∼30s).
  • 16
    • 0141766022 scopus 로고    scopus 로고
    • note
    • Comparing unaligned data sets, we found no significant correlation between the dwell time histograms for forward and backward directions of digestion (11). A cross-correlation analysis yielded a correlation coefficient r = 0.050 [-0.059, +0.159] over the region 605 to 1730 nm, where brackets denote the 95.4% statistical confidence interval determined by a bootstrap resampling analysis. The lack of a single dominant pause in the backward traces prevented us from making a robust backward alignment in that direction. Nevertheless, we attempted an alignment of backward traces, and cross-correlation between aligned forward and backward records yielded a correlation coefficient of r = -0.002 [-0.114, +0.110] over the region 595 to 1760 nm. All cross-correlations were computed over a region selected to contain a minimum of seven records in either direction (table S5).
  • 17
    • 0141431135 scopus 로고    scopus 로고
    • note
    • The estimated numbers of long pauses (>5 s) moving forwards and backwards were 49 and 19, respectively (for pauses >10 s, the corresponding numbers were 19 and 2). Estimates of the number of forward pauses were scaled by a factor of 0.62 to correct for the ratio of the total distance traveled moving forwards to backwards by all molecules scored over this region (675 to 1200 nm).
  • 20
    • 0035905687 scopus 로고    scopus 로고
    • P. R. Bianco et al., Nature 409, 374 (2001).
    • (2001) Nature , vol.409 , pp. 374
    • Bianco, P.R.1
  • 21
    • 0141766021 scopus 로고    scopus 로고
    • note
    • The single-molecule traces were aligned to 900 nm, which corresponds to a peak in the distribution of shifts necessary to align the traces. The average offset was -2.1 nm. If we aligned the traces so the average offset was O, then the dominant pause moved to 902.1 nm. In either case, the single-molecule data were within 2 nm of the gel-derived location.
  • 29
    • 0141654088 scopus 로고    scopus 로고
    • note
    • We thank K. Neuman and R. Knight for helpful discussions; E. Abbondanzieri for discussions and supplying his pause-finding algorithm; J. Einerson for extensive help with the assays; A. Engh, K. Herbert, and N. Padte for advice and help with sequencing gels; and U. Bali for the generous gift of lambda exonuclease. T.T.P. received support from a Burroughs Wellcome Fund Career Award in the Biomedical Sciences, a Princeton University Materials Institute Fellowship, and NIST. This work was supported by grants from the NIGMS GM 57035 (S.M.B.) and NHGRI HG 011821-01 (P.G.M.).


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.